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- PDB-1gs4: Structural basis for the glucocorticoid response in a mutant huma... -

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Basic information

Entry
Database: PDB / ID: 1gs4
TitleStructural basis for the glucocorticoid response in a mutant human androgen receptor (ARccr) derived from an androgen-independent prostate cancer
ComponentsANDROGEN RECEPTOR
KeywordsANDROGEN RECEPTOR / HUMAN ANDROGEN RECEPTOR / LIGAND-BINDING DOMAIN / CORTISOL/ CORTISONE RESPONSE / PROSTATE CANCER
Function / homology
Function and homology information


male somatic sex determination / prostate induction / lateral sprouting involved in mammary gland duct morphogenesis / male genitalia morphogenesis / regulation of developmental growth / POU domain binding / positive regulation of integrin biosynthetic process / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / androgen binding ...male somatic sex determination / prostate induction / lateral sprouting involved in mammary gland duct morphogenesis / male genitalia morphogenesis / regulation of developmental growth / POU domain binding / positive regulation of integrin biosynthetic process / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / androgen binding / cellular response to testosterone stimulus / regulation of systemic arterial blood pressure / Leydig cell differentiation / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / prostate gland epithelium morphogenesis / prostate gland growth / epithelial cell morphogenesis / membraneless organelle assembly / RNA polymerase II general transcription initiation factor binding / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of transcription by RNA polymerase III / morphogenesis of an epithelial fold / cellular response to steroid hormone stimulus / positive regulation of intracellular estrogen receptor signaling pathway / androgen receptor signaling pathway / seminiferous tubule development / RUNX2 regulates osteoblast differentiation / nuclear steroid receptor activity / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / regulation of protein localization to plasma membrane / intracellular receptor signaling pathway / estrogen receptor signaling pathway / steroid binding / insulin-like growth factor receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of cell differentiation / SUMOylation of intracellular receptors / molecular condensate scaffold activity / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / beta-catenin binding / Nuclear Receptor transcription pathway / positive regulation of miRNA transcription / transcription coactivator binding / multicellular organism growth / male gonad development / nuclear receptor activity / negative regulation of epithelial cell proliferation / cell-cell signaling / MAPK cascade / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / molecular adaptor activity / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / positive regulation of MAPK cascade / Ub-specific processing proteases / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / signaling receptor binding / negative regulation of cell population proliferation / positive regulation of cell population proliferation / chromatin binding / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Androgen receptor / Androgen receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Androgen receptor / Androgen receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / 9ALPHA-FLUOROCORTISOL / Androgen receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMatias, P.M. / Carrondo, M.A. / Coelho, R. / Thomaz, M. / Zhao, X.-Y. / Wegg, A. / Crusius, K. / Egner, U. / Donner, P.
CitationJournal: J.Med.Chem. / Year: 2002
Title: Structural Basis for the Glucocorticoid Response in a Mutant Human Androgen Receptor (Ar(Ccr)) Derived from an Androgen-Independent Prostate Cancer
Authors: Matias, P.M. / Carrondo, M.A. / Coelho, R. / Thomaz, M. / Zhao, X.-Y. / Wegg, A. / Crusius, K. / Egner, U. / Donner, P.
History
DepositionDec 27, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 28, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _citation.page_last / _entity_src_gen.pdbx_host_org_cell_line ..._citation.page_last / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANDROGEN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4153
Polymers28,9401
Non-polymers4752
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.350, 66.230, 73.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ANDROGEN RECEPTOR


Mass: 28939.934 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN, RESIDUES 670-917 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10275
#2: Chemical ChemComp-ZK5 / 9ALPHA-FLUOROCORTISOL


Mass: 380.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29FO5
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATIONS: LEU (491) HIS, THR (667) ALA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 41.3 %
Crystal growpH: 7.2 / Details: pH 7.20
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.4 M1reservoirNa2HPO4/2(H2O)
20.4 M1reservoirK2HPO4
30.1 MTris-maleate1reservoirpH9.5
45 %PEG2001reservoir
510 mMHEPES1droppH7.2
60.1 %n-octyl-beta-glucoside1drop
710 %glycerol1drop
810 nM9alpha-fluorocortisol1drop
9150 mM1dropLi2SO4
1010 mMdithiothreitol1drop
111 mMprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2001 / Details: TOROIDAL MIRRORS
RadiationMonochromator: DIAMOND(111)+GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.95→21.5 Å / Num. obs: 20504 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 18
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 4 / % possible all: 100
Reflection
*PLUS
Num. obs: 20515 / % possible obs: 99.9 % / Num. measured all: 74323
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E3G

1e3g


Resolution: 1.95→21.5 Å / Num. parameters: 8549 / Num. restraintsaints: 8331 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.285 998 5 %RANDOM 5% SUBSET
obs0.205 -100 %-
all-20504 --
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 1 / Occupancy sum non hydrogen: 2083
Refinement stepCycle: LAST / Resolution: 1.95→21.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 32 106 2132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.019
X-RAY DIFFRACTIONs_zero_chiral_vol0.027
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.15
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.073
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.205 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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